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- PDB-3wqj: Crystal structure of archaerhodopsin-2 at 1.8 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 3wqj
TitleCrystal structure of archaerhodopsin-2 at 1.8 angstrom resolution
ComponentsArchaerhodopsin-2
KeywordsTRANSPORT PROTEIN / 7 trans-membrane helices / light-driven proton pump
Function / homology
Function and homology information


monoatomic ion channel activity / photoreceptor activity / phototransduction / proton transmembrane transport / plasma membrane
Similarity search - Function
Bacterial rhodopsins retinal binding site. / Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BACTERIORUBERIN / 2,3-DI-PHYTANYL-GLYCEROL / Chem-L3P / Chem-L4P / RETINAL / Chem-SQL / Archaerhodopsin-2
Similarity search - Component
Biological speciesHalobacterium (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKouyama, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of archaerhodopsin-2 at 1.8 angstrom resolution.
Authors: Kouyama, T. / Fujii, R. / Kanada, S. / Nakanishi, T. / Chan, S.K. / Murakami, M.
History
DepositionJan 27, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Derived calculations
Category: citation / pdbx_struct_special_symmetry / struct_conn
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Archaerhodopsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6399
Polymers27,9541
Non-polymers4,6858
Water91951
1
A: Archaerhodopsin-2
hetero molecules

A: Archaerhodopsin-2
hetero molecules

A: Archaerhodopsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,91627
Polymers83,8613
Non-polymers14,05524
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area23960 Å2
ΔGint-178 kcal/mol
Surface area23540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.739, 62.739, 331.464
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-308-

SQL

21A-308-

SQL

31A-308-

SQL

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Archaerhodopsin-2 / AR 2


Mass: 27953.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halobacterium (Halophile) / Strain: AUS-2 / References: UniProt: P29563

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Non-polymers , 8 types, 59 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-22B / BACTERIORUBERIN


Mass: 741.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C50H76O4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-L2P / 2,3-DI-PHYTANYL-GLYCEROL / 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL


Mass: 653.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H88O3
#6: Chemical ChemComp-L3P / 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE


Mass: 885.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H94O11P2
#7: Chemical ChemComp-L4P / 3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL / 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL


Mass: 807.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C46H95O8P
#8: Chemical ChemComp-SQL / (6E,10E,14E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene / squalene


Mass: 410.718 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H50
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.8M AMMONIUM SULFATE, 0.1M HEPES, 0.32% NONYLGLUCOSIDE, 8% trehalose, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2013
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→45.11 Å / Num. all: 24035 / Num. obs: 21944 / % possible obs: 91.3 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 / Redundancy: 8.8 % / Biso Wilson estimate: 23.15 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 28.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 5.1 / Num. unique all: 3460 / Rsym value: 0.5 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EI4

2ei4


Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.996 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1105 5.1 %RANDOM
Rwork0.2112 20596 --
obs0.2127 21701 90.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 102.68 Å2 / Biso mean: 26.661 Å2 / Biso min: 11.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20.47 Å20 Å2
2--0.94 Å20 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 180 51 2041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222025
X-RAY DIFFRACTIONr_angle_refined_deg2.0332.0492742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9175233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.43921.58763
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.50315291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2481511
X-RAY DIFFRACTIONr_chiral_restr0.2210.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021400
X-RAY DIFFRACTIONr_mcbond_it0.9831.51152
X-RAY DIFFRACTIONr_mcangle_it1.70421851
X-RAY DIFFRACTIONr_scbond_it2.7293873
X-RAY DIFFRACTIONr_scangle_it4.2054.5891
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 103 -
Rwork0.305 1629 -
all-1732 -
obs--99.26 %

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